Welcome to my research page. I've tried to link to stable repositories. If you find something that's broken or incorrect, or you simply would like more information, please let me know. The bibtex entries are not uniform, but I've tried to keep to either ACM or DBLP. In a few cases, like the XML conferences, the proceedings are available only online, so I've created my own to share. I haven't included posters--those can be found in my CV. We have begun upgrading our OSs this summer (2006), so some projects might be slightly unstable.
Edited Journals/Collections
-
[Sun Kim], Zhiping Wang, and Mehmet M. Dalkilic 
iGibbs: A Motif Discovery Framework for Gibbs Sampling Algorithm
Proteins: Structure, Function, and Bioinformatics (2007) 66(3):671-681 - Abstract Proteins: Structure, Function, and Bioinformatics (10.1002/prot.21153)
- [Rupali Patwardhan], [Haixu Tang] ,[Sun Kim], and Mehmet M. Dalkilic
- An Approximate de Bruijn Graph Approach to Multiple Local alignment and Motif Discovery in Protein Sequences
- 1st VLDB Workshop on Data mining in Bioinformatics, LNCS (2006), Mehmet M. Dalkilic, Sun Kim, and Jiong Yang Eds.
- Abstract PDF
- [Christopher Mueller],
Mehmet M. Dalkilic, and [Andrew Lumsdaine]
- High-Performance Direct Pairwise Comparison of Large
Genomic Sequences
- A special issue of IEEE Transactions on Parallel and Distributed Systems of computational biology,
August (2006) 17(8):764-772, ISSN 1045-9219
- Abstract not yet available PDF not yet available
- [Henry M. Kim], [Arijit Sengupta] ,[Mark S. Fox], and Mehmet M. Dalkilic
- A Measurement Ontology Generalizable for Emerging Domain Applications on the Web
- Journal of Database Management (2005) 18(1):20-42
- Abstract JDB PDF(not for distribution)
- [DoHoon Lee], [Jeong-Hyeon Choi ],
Mehmet M. Dalkilic, and [Sun Kim]
- COMPAM :visualization of combining pairwise alignments for multiple genomes
- Bioinformatics (2005) 22(2):442-444, PMID: 16269416)
- Abstract PDF
- Mehmet M. Dalkilic, [Edward Robertson], and [Dirk Van Gucht]
- {Chapter} CE: The Classifier-Estimator Framework for Data Mining
- {Title} Data Mining and Reverse Engineering. Chapman & Hall (1998) 520 p., Stefano Spaccapietra and Fred Maryanski, Fred (Eds.) Hardcover ISBN: 0-412-82250-4.
- [James C. Costello],
[Jade Buchannan-Carter], Mehmet Dalkilic, and
[Justen Andrews]
- Integrating Drosophila Data to Discover Disease-Related Protein Interactions in Human
- IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. (2007) to appear
- Abstract PDF {to appear}
- [Rupali Patwardhan], [Haixu Tang] ,[Sun Kim], and Mehmet M. Dalkilic
- An Approximate de Bruijn Graph Approach to Multiple Local alignment and Motif Discovery in Protein Sequences
- 1st VLDB Workshop on Data mining in Bioinformatics {to appear}
- Abstract not yet available PDF not yet available
- Mehmet M. Dalkilic, [Wyatt T. Clark],
[James C. Costello], and [Predrag Radivojac]
- Using Compression to Identify Classes of Inauthentic Texts
- SIAM Conference on Data Mining (2006) pp.603-607 /li>
- Abstract PDF {extended version} bibtex
- Transforming Biology into an Information Science (Short paper)
- i-Conference The Pennsylvania State University, PE (2005)
- Mehmet M. Dalkilic, [Sun Kim], [Predrag Radivojac], and [Haixu Tang]
- Abstract
- James Costello, Mehmet Dalkilic, Rupali Patwardhan, Sumit Middha, Brian Eads, John Colbourne, Junguk Hur, Keval Mehta, and Justen Andrews
- Network Properties of a Gene Network Built from Drosophila melanogaster Data (NetSci 2006
- [Christopher Mueller],
Mehmet M. Dalkilic, and [Andrew Lumsdaine]
- High-Performance Direct Pairwise Comparison of Large Genomic Sequences
- Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology, April 5 (HiCOMB 2005) p 199.
- Proceedings Abstract PDF
- Mehmet M. Dalkilic
- An Architecture and Application for Integrating Curation Data at the
Residue Level for Proteins
- Data Integration in the Life Sciences, Second International
Workshop. Lecture Notes In Computer Science; Vol. 3615. San Diego, CA, July 20-22
(2005) pp. 335-338, ISBN: 3-540-27967-9
Proceedings.
- bibtex PDF not available
- Mehmet M. Dalkilic and [Arijit Sengupta]
- Design and evaluation of CATPA: curation and alignment tool for protein analysis
- SAC '05: Proceedings of the 2005 ACM symposium on Applied computing, Track: Bioinformatics, Santa Fe, New Mexico (2005) pp. 190-194, ISBN: 1-58113-964-0
Proceedings.
- Abstract bibtex PDF
- Mehmet M. Dalkilic and [Arijit Sengupta]
- Circle: design and implementation of a classifier based on circuit minimization (Short paper)
- SAC '05: Proceedings of the 2005 ACM symposium on Applied computing, Track: Data Mining, Santa Fe, New Mexico (2005) pp. 547-548, ISBN: 1-58113-964-0
Proceedings.
- Abstract bibtex PDF
- Mehmet M. Dalkilic and [Arijit Sengupta]
- Semantic Thumbnails: Summarizing XML Documents for the Semantic Web
- In Proceedings, XML 2004 Conference, Washington, DC. November 15-19 (2004) (Available directly from XML 2004 Online Proceedings).
Proceedings.
- Abstract bibtex PDF
- Zhiping Wang, Mehmet M. Dalkilic and [Sun Kim]
- Guiding motif discovery by iterative pattern refinement
- Proceedings of the 2004 ACM symposium on Applied computing, SESSION: Bioinformatics (BIO)
Nicosia, Cyprus (2004) pp. 162-166,
ISBN:1-58113-812-1
Proceedings.
- Abstract bibtex PDF
- Mehmet M. Dalkilic and [James Costello]
- BioKnOT: Biological Knowledge through Ontologies and TFIDF
- in SIGIR Bioinformatics Workshop in conjunction with SIGIR Sheffield, UK (2004)
Proceedings.
- Abstract bibtex PDF
- [Arijit Sengupta], Mehmet M. Dalkilic and [James Costello]
- Semantic thumbnails: a novel method for summarizing document collections
- ACM Special Interest Group for Design of Communications. Proceedings of the 22nd annual international conference on Design of communication: The engineering of quality documentation. Memphis, Tennessee, USA (2004) pp 45-51,
ISBN: 1-58113-809-1
Proceedings.
- Abstract bibtex PDF
- [Irfan Gunduz], [Sihui Zhao], Mehmet Dalkilic and [Sun Kim]
- Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsis thaliana
- Proceedings of the International Conference on Mathematics
and Engineering Techniques in Medicine and Biological Scienes,
METMBS '03, Las Vegas, Nevada, USA, June 23 - 26, (2003) pp 29-34, ISBN: 1-932415-04-1. Faramarz Valafar and
Homayoun Valafar (Eds.)
Proceedings
- Abstract bibtex PDF
- [Arijit Sengupta] and Mehmet M. Dalkilic,
- DSQL--an SQL for structured documents
Extended Abstract
- Lecture Notes in Computer Science; Vol. 2348. Proceedings of Advanced Information Systems Engineering, 14th International
Conference, CAiSE 2002, Toronto, Canada, May 27-31, (2002) pp 757-760, ISBN: 3-540-43738-X. Anne Banks Pidduck, John Mylopoulos,Carson C. Woo, and
M. Tamer Özsu (Eds.) Proceedings
- Abstract bibtex PDF
- [Chris Giannella], Mehmet M. Dalkilic, [Dennis Groth], and [Edward Robertson]
- Improving Query Evaluation with Approximate Functional Dependency Based Decompositions
- Lecture Notes In Computer Science; Vol. 2405. Proceedings of the 19th British National Conference on Databases: Advances in Databases
BNCOD 19, Sheffield, UK, July 17-19 (2002) pp 26-41,
ISBN:3-540-43905-6. Proceedings
- Abstract bibtex PDF
- Mehmet M. Dalkilic and [Edward Robertson]
- Information Dependencies
- In Proceedings of the 19th ACM SIGMOD-SIGACT-SIGART Symposium on Principals of Database Systems
(PODS) (2000) pp 245-253
Proceedings.
- Abstract bibtex PDF
- Mehmet M. Dalkilic, [Edward Robertson], and [Dirk Van Gucht]
- CE: The Classifier-Estimator Framework for Data Mining
- Data Mining and Reverse Engineering: Searching for Semantics, IFIP TC2/WG2.6 Seventh Conference on Database Semantics (DS-7), Leysin, Switzerland
October 7-10, (1997) pp 89-104. Proceedings.
- Abstract bibtex PDF
- Mehmet M. Dalkilic, Manoj Jain, Dirk Van Gucht, and Anurag Mendhekar
- Design and Implementation of Reflective SQL
- Abstract bibtex PDF
Application
Application
Bibtex
Refereed Conferences and Workshops
Technical Reports & Invited Talks